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  1. AU="Lee, Brian H"
  2. AU="May, Susann"
  3. AU="Remondes-Costa, Sónia"
  4. AU="Lauren Sauer"
  5. AU="G Saiz, Paula"
  6. AU="Stoica, George"
  7. AU=Odorizzi Pamela M.
  8. AU=Pollaers Katherine
  9. AU="Stefanova, Veselina"
  10. AU="Geraldine M. O’Connor"
  11. AU="Jim E. Banta"
  12. AU="Marti-Bonmati, Luis"
  13. AU="Doris Kampner"
  14. AU="Luca Soraci"

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  1. Buch ; Online: Lennard Jones Token

    Lee, Brian H. / Strachan, Alejandro

    a blockchain solution to scientific data curation

    2023  

    Abstract: Data science and artificial intelligence have become an indispensable part of scientific research. While such methods rely on high-quality and large quantities of machine-readable scientific data, the current scientific data infrastructure faces ... ...

    Abstract Data science and artificial intelligence have become an indispensable part of scientific research. While such methods rely on high-quality and large quantities of machine-readable scientific data, the current scientific data infrastructure faces significant challenges that limit effective data curation and sharing. These challenges include insufficient return on investment for researchers to share quality data, logistical difficulties in maintaining long-term data repositories, and the absence of standardized methods for evaluating the relative importance of various datasets. To address these issues, this paper presents the Lennard Jones Token, a blockchain-based proof-of-concept solution implemented on the Ethereum network. The token system incentivizes users to submit optimized structures of Lennard Jones particles by offering token rewards, while also charging for access to these valuable structures. Utilizing smart contracts, the system automates the evaluation of submitted data, ensuring that only structures with energies lower than those in the existing database for a given cluster size are rewarded. The paper explores the details of the Lennard Jones Token as a proof of concept and proposes future blockchain-based tokens aimed at enhancing the curation and sharing of scientific data.
    Schlagwörter Computer Science - Networking and Internet Architecture ; Condensed Matter - Materials Science
    Thema/Rubrik (Code) 306
    Erscheinungsdatum 2023-12-01
    Erscheinungsland us
    Dokumenttyp Buch ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  2. Artikel ; Online: Acquisition, Processing, and Quality Control of Mass Cytometry Data.

    Lee, Brian H / Rahman, Adeeb H

    Methods in molecular biology (Clifton, N.J.)

    2019  Band 1989, Seite(n) 13–31

    Abstract: Mass cytometry uniquely combines the principles of mass spectrometry and flow cytometry for high dimensional profiling of immune cells at a single cell level. Using isotopically conjugated antibodies, mass cytometry overcomes the limitations of spectral ... ...

    Abstract Mass cytometry uniquely combines the principles of mass spectrometry and flow cytometry for high dimensional profiling of immune cells at a single cell level. Using isotopically conjugated antibodies, mass cytometry overcomes the limitations of spectral overlap associated with flow cytometry and allows for deeper single cell characterization of complex biospecimens using more cellular markers. However, the nature of mass spectrometry-based single cell measurements requires specific considerations in acquiring and processing data. This chapter provides an overview of how to optimally acquire mass cytometry data and how to process this data for subsequent analysis and characterization of cell populations.
    Mesh-Begriff(e) Biomarkers/analysis ; Cells/cytology ; Flow Cytometry/methods ; Humans ; Mass Spectrometry/methods ; Quality Control ; Single-Cell Analysis/methods ; Staining and Labeling/methods
    Chemische Substanzen Biomarkers
    Sprache Englisch
    Erscheinungsdatum 2019-05-10
    Erscheinungsland United States
    Dokumenttyp Journal Article
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-4939-9454-0_2
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  3. Artikel ; Online: Different chromatin and DNA sequence characteristics define glucocorticoid receptor binding sites that are blocked or not blocked by coregulator Hic-5.

    Lee, Brian H / Stallcup, Michael R

    PloS one

    2018  Band 13, Heft 5, Seite(n) e0196965

    Abstract: The glucocorticoid receptor (GR) regulates genes in many physiological pathways by binding to enhancer and silencer elements of target genes, where it recruits coregulator proteins that remodel chromatin and regulate the assembly of transcription ... ...

    Abstract The glucocorticoid receptor (GR) regulates genes in many physiological pathways by binding to enhancer and silencer elements of target genes, where it recruits coregulator proteins that remodel chromatin and regulate the assembly of transcription complexes. The coregulator Hydrogen peroxide-inducible clone 5 (Hic-5) is necessary for glucocorticoid (GC) regulation of one group of GR target genes, is irrelevant for a second group, and inhibits GR binding to a third gene set, thereby blocking their regulation by GC. Gene-specific characteristics that distinguish GR binding regions (GBR) at Hic-5 blocked genes from GBR at other GC-regulated genes are unknown. Here we show genome-wide that blocked GBR generally require CHD9 and BRM for GR occupancy in contrast to GBR that are not blocked by Hic-5. Hic-5 blocked GBR are enriched near Hic-5 blocked GR target genes but not near GR target genes that are not blocked by Hic-5. Furthermore blocked GBR are in a closed conformation prior to Hic-5 depletion, and require Hic-5 depletion and glucocorticoid treatment to create an open conformation necessary for GR occupancy. A transcription factor binding motif characteristic of the ETS family was enriched near blocked GBR and blocked genes but not near non-blocked GBR or non-blocked GR target genes. Thus, we identify specific differences in chromatin conformation, chromatin remodeler requirements, and local DNA sequence motifs that contribute to gene-specific actions of transcription factors and coregulators. These findings shed light on mechanisms that contribute to binding site selection by transcription factors, which vary in a cell type-specific manner.
    Mesh-Begriff(e) Base Sequence/genetics ; Binding Sites ; Cell Line, Tumor ; Cell Lineage/genetics ; Chromatin/genetics ; Chromatin Assembly and Disassembly/genetics ; DNA Helicases ; DNA-Binding Proteins/genetics ; Gene Expression Regulation/genetics ; Genome/genetics ; Glucocorticoids/genetics ; Humans ; LIM Domain Proteins/genetics ; Nucleotide Motifs/genetics ; Protein Binding ; Receptors, Glucocorticoid/genetics ; Trans-Activators ; Transcription Factors/genetics ; Transcription, Genetic
    Chemische Substanzen Chromatin ; DNA-Binding Proteins ; Glucocorticoids ; LIM Domain Proteins ; NR3C1 protein, human ; Receptors, Glucocorticoid ; SMARCA2 protein, human ; Trans-Activators ; Transcription Factors ; DNA Helicases (EC 3.6.4.-) ; CHD9 protein, human (EC 3.6.4.12)
    Sprache Englisch
    Erscheinungsdatum 2018-05-08
    Erscheinungsland United States
    Dokumenttyp Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ISSN 1932-6203
    ISSN (online) 1932-6203
    DOI 10.1371/journal.pone.0196965
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  4. Artikel ; Online: Glucocorticoid receptor binding to chromatin is selectively controlled by the coregulator Hic-5 and chromatin remodeling enzymes.

    Lee, Brian H / Stallcup, Michael R

    The Journal of biological chemistry

    2017  Band 292, Heft 22, Seite(n) 9320–9334

    Abstract: The steroid hormone-activated glucocorticoid receptor (GR) regulates cellular stress pathways by binding to genomic regulatory elements of target genes and recruiting coregulator proteins to remodel chromatin and regulate transcription complex assembly. ... ...

    Abstract The steroid hormone-activated glucocorticoid receptor (GR) regulates cellular stress pathways by binding to genomic regulatory elements of target genes and recruiting coregulator proteins to remodel chromatin and regulate transcription complex assembly. The coregulator hydrogen peroxide-inducible clone 5 (Hic-5) is required for glucocorticoid (GC) regulation of some genes but not others and blocks the regulation of a third gene set by inhibiting GR binding. How Hic-5 exerts these gene-specific effects and specifically how it blocks GR binding to some genes but not others is unclear. Here we show that site-specific blocking of GR binding is due to gene-specific requirements for ATP-dependent chromatin remodeling enzymes. By depletion of 11 different chromatin remodelers, we found that ATPases chromodomain helicase DNA-binding protein 9 (CHD9) and Brahma homologue (BRM, a product of the SMARCA2 gene) are required for GC-regulated expression of the blocked genes but not for other GC-regulated genes. Furthermore, CHD9 and BRM were required for GR occupancy and chromatin remodeling at GR-binding regions associated with blocked genes but not at GR-binding regions associated with other GC-regulated genes. Hic-5 selectively inhibits GR interaction with CHD9 and BRM, thereby blocking chromatin remodeling and robust GR binding at GR-binding sites associated with blocked genes. Thus, Hic-5 regulates GR binding site selection by a novel mechanism, exploiting gene-specific requirements for chromatin remodeling enzymes to selectively influence DNA occupancy and gene regulation by a transcription factor.
    Mesh-Begriff(e) Cell Line, Tumor ; Chromatin/genetics ; Chromatin/metabolism ; Chromatin Assembly and Disassembly/physiology ; DNA Helicases ; DNA-Binding Proteins/genetics ; DNA-Binding Proteins/metabolism ; Humans ; Intracellular Signaling Peptides and Proteins/genetics ; Intracellular Signaling Peptides and Proteins/metabolism ; LIM Domain Proteins/genetics ; LIM Domain Proteins/metabolism ; Receptors, Glucocorticoid/genetics ; Receptors, Glucocorticoid/metabolism ; Trans-Activators ; Transcription Factors/genetics ; Transcription Factors/metabolism
    Chemische Substanzen Chromatin ; DNA-Binding Proteins ; Intracellular Signaling Peptides and Proteins ; LIM Domain Proteins ; Receptors, Glucocorticoid ; SMARCA2 protein, human ; TGFB1I1 protein, human ; Trans-Activators ; Transcription Factors ; DNA Helicases (EC 3.6.4.-) ; CHD9 protein, human (EC 3.6.4.12)
    Sprache Englisch
    Erscheinungsdatum 2017-04-05
    Erscheinungsland United States
    Dokumenttyp Journal Article
    ZDB-ID 2997-x
    ISSN 1083-351X ; 0021-9258
    ISSN (online) 1083-351X
    ISSN 0021-9258
    DOI 10.1074/jbc.M117.782607
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  5. Buch ; Online: Mapping microstructure to shock-induced temperature fields using deep learning

    Li, Chunyu / Verduzco, Juan Carlos / Lee, Brian H. / Appleton, Robert J. / Strachan, Alejandro

    2023  

    Abstract: The response of materials to dynamical, or shock, loading is important to planetary science, aerospace engineering, and energetic materials. Thermal-activated processes, including chemical reactions and phase transitions, are significantly accelerated by ...

    Abstract The response of materials to dynamical, or shock, loading is important to planetary science, aerospace engineering, and energetic materials. Thermal-activated processes, including chemical reactions and phase transitions, are significantly accelerated by the localization of the energy deposited into hotspots. These results from the interaction of a supersonic wave with the materials microstructure and are governed by complex, coupled processes, including the collapse of porosity, interfacial friction, and localized plastic deformation. These mechanisms are not fully understood and today we lack predictive models to, for example, predict the shock to detonation transition from chemistry and microstructure alone. We demonstrate that deep learning techniques can be used to predict the resulting shock-induced temperature fields in complex composite materials obtained from large-scale molecular dynamics simulations with the initial microstructure as the only input. The accuracy of the Microstructure-Informed Shock-induced Temperature net (MISTnet) model is higher than the current state of the art at a fraction of the computation cost.
    Schlagwörter Condensed Matter - Materials Science
    Thema/Rubrik (Code) 669
    Erscheinungsdatum 2023-03-30
    Erscheinungsland us
    Dokumenttyp Buch ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  6. Artikel: Retrospective Clinical Evaluation of a Decision-Support Software for Adaptive Radiotherapy of Head and Neck Cancer Patients.

    Gros, Sebastien A A / Santhanam, Anand P / Block, Alec M / Emami, Bahman / Lee, Brian H / Joyce, Cara

    Frontiers in oncology

    2022  Band 12, Seite(n) 777793

    Abstract: Purpose: This study aimed to evaluate the clinical need for an automated decision-support software platform for adaptive radiation therapy (ART) of head and neck cancer (HNC) patients.: Methods: We tested RTapp (SegAna), a new ART software platform ... ...

    Abstract Purpose: This study aimed to evaluate the clinical need for an automated decision-support software platform for adaptive radiation therapy (ART) of head and neck cancer (HNC) patients.
    Methods: We tested RTapp (SegAna), a new ART software platform for deciding when a treatment replan is needed, to investigate a set of 27 HNC patients' data retrospectively. For each fraction, the software estimated key components of ART such as daily dose distribution and cumulative doses received by targets and organs at risk (OARs) from daily 3D imaging in real-time. RTapp also included a prediction algorithm that analyzed dosimetric parameter (DP) trends against user-specified thresholds to proactively trigger adaptive re-planning up to four fractions ahead. The DPs evaluated for ART were based on treatment planning dose constraints. Warning (V
    Results: RTapp was able to address the needs of treatment adaptation. Specifically, we identified 18/27 studies (67%) for violating PTV coverage or parotid D
    Conclusion: Integrated in an ART clinical workflow, RTapp aids in predicting whether specific treatment would require adaptation up to four fractions ahead of time.
    Sprache Englisch
    Erscheinungsdatum 2022-06-30
    Erscheinungsland Switzerland
    Dokumenttyp Journal Article
    ZDB-ID 2649216-7
    ISSN 2234-943X
    ISSN 2234-943X
    DOI 10.3389/fonc.2022.777793
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  7. Artikel: Single-cell RNA sequencing identifies distinct transcriptomic signatures between PMA/ionomycin- and αCD3/αCD28-activated primary human T cells.

    Lee, Jung Ho / Lee, Brian H / Jeong, Soyoung / Joh, Christine Suh-Yun / Nam, Hyo Jeong / Choi, Hyun Seung / Sserwadda, Henry / Oh, Ji Won / Park, Chung-Gyu / Jin, Seon-Pil / Kim, Hyun Je

    Genomics & informatics

    2023  Band 21, Heft 2, Seite(n) e18

    Abstract: Immunologists have activated T cells in vitro using various stimulation methods, including phorbol myristate acetate (PMA)/ionomycin and αCD3/αCD28 agonistic antibodies. PMA stimulates protein kinase C, activating nuclear factor-κB, and ionomycin ... ...

    Abstract Immunologists have activated T cells in vitro using various stimulation methods, including phorbol myristate acetate (PMA)/ionomycin and αCD3/αCD28 agonistic antibodies. PMA stimulates protein kinase C, activating nuclear factor-κB, and ionomycin increases intracellular calcium levels, resulting in activation of nuclear factor of activated T cell. In contrast, αCD3/αCD28 agonistic antibodies activate T cells through ZAP-70, which phosphorylates linker for activation of T cell and SH2-domain-containing leukocyte protein of 76 kD. However, despite the use of these two different in vitro T cell activation methods for decades, the differential effects of chemical-based and antibody-based activation of primary human T cells have not yet been comprehensively described. Using single-cell RNA sequencing (scRNA-seq) technologies to analyze gene expression unbiasedly at the single-cell level, we compared the transcriptomic profiles of the non-physiological and physiological activation methods on human peripheral blood mononuclear cell-derived T cells from four independent donors. Remarkable transcriptomic differences in the expression of cytokines and their respective receptors were identified. We also identified activated CD4 T cell subsets (CD55+) enriched specifically by PMA/ionomycin activation. We believe this activated human T cell transcriptome atlas derived from two different activation methods will enhance our understanding, highlight the optimal use of these two in vitro T cell activation assays, and be applied as a reference standard when analyzing activated specific disease-originated T cells through scRNA-seq.
    Sprache Englisch
    Erscheinungsdatum 2023-06-30
    Erscheinungsland Korea (South)
    Dokumenttyp Journal Article
    ZDB-ID 2802682-2
    ISSN 2234-0742 ; 1598-866X
    ISSN (online) 2234-0742
    ISSN 1598-866X
    DOI 10.5808/gi.23009
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  8. Artikel ; Online: A simple dosimetric approach to spatially fractionated GRID radiation therapy using the multileaf collimator for treatment of breast cancers in the prone position.

    Murphy, Natasha L / Philip, Rino / Wozniak, Matt / Lee, Brian H / Donnelly, Eric D / Zhang, Hualin

    Journal of applied clinical medical physics

    2020  Band 21, Heft 11, Seite(n) 105–114

    Abstract: The purpose of this study was to explore the treatment planning methods of spatially fractionated radiation therapy (SFRT), commonly referred to as GRID therapy, in the treatment of breast cancer patients using multileaf collimator (MLC) in the prone ... ...

    Abstract The purpose of this study was to explore the treatment planning methods of spatially fractionated radiation therapy (SFRT), commonly referred to as GRID therapy, in the treatment of breast cancer patients using multileaf collimator (MLC) in the prone position. A total of 12 patients with either left or right breast cancer were retrospectively chosen. The computed tomography (CT) images taken for the whole breast external beam radiation therapy (WB-EBRT) were used for GRID therapy planning. Each GRID plan was made by using two portals and each portal had two fields with 1-cm aperture size. The dose prescription point was placed at the center of the target volume, and a dose of 20 Gy with 6-MV beams was prescribed. Dose-volume histogram (DVH) curves were generated to evaluate dosimetric properties. A modified linear-quadratic (MLQ) radiobiological response model was used to assess the equivalent uniform doses (EUD) and therapeutic ratios (TRs) of all GRID plans. The DVH curves indicated that these MLC-based GRID therapy plans can deliver heterogeneous dose distribution in the target volume as seen with the conventional cerrobend GRID block. The plans generated by the MLC technique also demonstrated the advantage for accommodating different target shapes, sparing normal structures, and reporting dose metrics to the targets and the organs at risks. All GRID plans showed to have similar dosimetric parameters, implying the plans can be made in a consistent quality regardless of the shape of the target and the size of volume. The mean dose of lung and heart were respectively below 0.6 and 0.7 Gy. When the size of aperture is increased from 1 to 2 cm, the EUD and TR became smaller, but the peak/valley dose ratio (PVDR) became greater. The dosimetric approach of this study was proven to be simple, practical and easy to be implemented in clinic.
    Mesh-Begriff(e) Breast Neoplasms/radiotherapy ; Female ; Humans ; Prone Position ; Radiometry ; Radiotherapy Dosage ; Radiotherapy Planning, Computer-Assisted ; Retrospective Studies
    Sprache Englisch
    Erscheinungsdatum 2020-10-29
    Erscheinungsland United States
    Dokumenttyp Journal Article
    ZDB-ID 2010347-5
    ISSN 1526-9914 ; 1526-9914
    ISSN (online) 1526-9914
    ISSN 1526-9914
    DOI 10.1002/acm2.13040
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  9. Artikel ; Online: The Clinical Utility of MRI in Evaluating for Osteomyelitis in Patients Presenting with Uncomplicated Cellulitis.

    Klein, Devon A / Lee, Brian H / Bezhani, Hariklia / Droukas, Daniel D / Stoffels, Guillaume

    The Journal of foot and ankle surgery : official publication of the American College of Foot and Ankle Surgeons

    2020  Band 59, Heft 2, Seite(n) 323–329

    Abstract: Magnetic resonance imaging (MRI) is vital in the diagnosis of osteomyelitis (OM) in patients presenting with cellulitis. Typically, cellulitis is treated with oral antibiotics; however, patients with concomitant OM may require long-term intravenous ... ...

    Abstract Magnetic resonance imaging (MRI) is vital in the diagnosis of osteomyelitis (OM) in patients presenting with cellulitis. Typically, cellulitis is treated with oral antibiotics; however, patients with concomitant OM may require long-term intravenous antibiotics or surgical intervention. We reviewed lower extremity MRIs in patients presenting with cellulitis and clinical concern for OM. We found 488 patient examinations spanning 5 years (2011 to 2016); 47 patients were excluded (final N = 441). Each MRI was interpreted by a radiologist to determine the rate of OM, abscess, ulceration, and imaging diagnosis of cellulitis. Concurrent assessment of the electronic medical record was performed to review patient demographics, the presence of abscess and/or ulceration, and comorbidities such as diabetes, hyperlipidemia (HLD), atherosclerotic disease, and peripheral vascular disease. Of the 441 lower extremity MRIs included, 170 (39%) were diagnosed with OM, 236 (54%) had ulcers, and 66 (15%) had abscesses. Age, laterality, and reporting physician were not statistically significant independent variables in the rate of reported OM. Diabetes and HLD/atherosclerotic disease were both statistically significant variables with regard to OM rates. Clinical documentation and MRI diagnosis of ulceration were both statistically significant variables in the rate of OM. Regression analysis determined that body part, ulceration, HLD/atherosclerosis, and sex were independent predictors of OM. In our study, of the population of patients with a high clinical suspicion for OM, 39% had OM diagnosed on MRI. However, the incidence of OM in uncomplicated cellulitis was only 11.8% compared with 43.9% in complicated cellulitis. When considering the forefoot alone, patients with ulceration at MRI were 5.6 times more likely to have underlying OM than those without.
    Mesh-Begriff(e) Adult ; Aged ; Aged, 80 and over ; Cellulitis/complications ; Cellulitis/diagnosis ; Female ; Humans ; Lower Extremity/diagnostic imaging ; Magnetic Resonance Imaging/statistics & numerical data ; Male ; Middle Aged ; Osteomyelitis/diagnosis ; Osteomyelitis/etiology ; Reproducibility of Results ; Retrospective Studies ; Young Adult
    Sprache Englisch
    Erscheinungsdatum 2020-03-04
    Erscheinungsland United States
    Dokumenttyp Journal Article
    ZDB-ID 1146972-9
    ISSN 1542-2224 ; 1067-2516
    ISSN (online) 1542-2224
    ISSN 1067-2516
    DOI 10.1053/j.jfas.2019.02.009
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  10. Artikel ; Online: Hippocampus sparing volumetric modulated arc therapy in patients with loco-regionally advanced oropharyngeal cancer.

    Seol, Seung Won / Lee, Brian H / Sita, Timothy L / Devineni, Jay Ram / Kruser, Tim J / Sachdev, Sean / Gentile, Michelle / Helenowski, Irene / Mittal, Bharat B

    Physics and imaging in radiation oncology

    2022  Band 24, Seite(n) 71–75

    Abstract: This study aimed to assess the incidental radiation exposure of the hippocampus (HC) in locoregionally-advanced oropharyngeal cancer patients undergoing volumetric modulated arc therapy and the feasibility of HC-sparing plan optimization. The initial ... ...

    Abstract This study aimed to assess the incidental radiation exposure of the hippocampus (HC) in locoregionally-advanced oropharyngeal cancer patients undergoing volumetric modulated arc therapy and the feasibility of HC-sparing plan optimization. The initial plans were generated without dose-volume constraints to the HC and were compared with the HC-sparing plans. The incidental D
    Sprache Englisch
    Erscheinungsdatum 2022-09-24
    Erscheinungsland Netherlands
    Dokumenttyp Journal Article
    ISSN 2405-6316
    ISSN (online) 2405-6316
    DOI 10.1016/j.phro.2022.09.008
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